Molecular Dynamics simulations have been carried out on systems of increasing complexity and biological relevance, in particular aqueous solutions of ions and peptides, in order to establish the local association patterns of solute and solvent molecules, as well as the structure formed by the solvent around the solvated ions/molecules. To account for quantum effects not readily observed in classical MD, ab initio Car-Parrinello simulations have been carried out. To establish a connection with experimental findings and thus underpin simulation results, techniques were developed to compute and refine structure factors from simulations to compare with experimental scattering data. Based on these findings, water models’ qualities as a solvent have been evaluated, resulting in a firm disinclination to the TIP3P model. Further tools to quantify local structure have been developed and implemented, including the development of an order parameter to gauge the four-fold co-ordination of water in pure and mixed form as a function of a parameter of interest, here temperature, and special density calculations to visualise the local neighbourhood of molecules. A key objective was to elucidate previously disputed areas in the fundamental findings surrounding the systems in question. This has been achieved in the case of aqueous solution of L-proline with regards to the formation of macromolecular association and the formation of intermediate structure, as well as the question of close ion contact and local ion solvation structure and co-ordination of aqueous NaCl. Beyond that, new insight into the mechanism of exchange of members of the first solvation shell of Na, as well as into the molecular mechanism based on the hydrogen bonding pattern of inter-proline and proline-water association as a facilitator to the cryoprotectant nature of proline was gained. Finally, the nature of the helix formed by the gp41 polypeptide in water was expounded.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:663048 |
| Date | January 2007 |
| Creators | Troitzsch, Raphael Zacharias |
| Publisher | University of Edinburgh |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://hdl.handle.net/1842/14581 |
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